Multiple sequence alignment - TraesCS3B01G363900

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3B01G363900 chr3B 100.000 2585 0 0 1 2585 575756190 575753606 0 4774
1 TraesCS3B01G363900 chr7A 97.895 1995 41 1 592 2585 60107873 60105879 0 3450
2 TraesCS3B01G363900 chr7A 97.980 594 12 0 1 594 60108502 60107909 0 1031
3 TraesCS3B01G363900 chr5A 97.895 1995 41 1 592 2585 73030715 73032709 0 3450
4 TraesCS3B01G363900 chr5A 97.811 594 13 0 1 594 73030086 73030679 0 1026
5 TraesCS3B01G363900 chr1B 97.644 1995 46 1 592 2585 638750886 638748892 0 3422
6 TraesCS3B01G363900 chr1B 97.980 594 12 0 1 594 638751515 638750922 0 1031
7 TraesCS3B01G363900 chr2D 97.494 1995 48 2 592 2585 637322006 637320013 0 3406
8 TraesCS3B01G363900 chr2D 96.540 1994 66 2 592 2582 189854086 189856079 0 3297
9 TraesCS3B01G363900 chr2D 97.663 599 9 1 1 594 635050985 635051583 0 1024
10 TraesCS3B01G363900 chr3D 97.093 1995 56 2 592 2585 523758739 523760732 0 3362
11 TraesCS3B01G363900 chr2B 96.842 1995 62 1 592 2585 500713242 500715236 0 3334
12 TraesCS3B01G363900 chr2B 98.316 594 10 0 1 594 500712613 500713206 0 1042
13 TraesCS3B01G363900 chr6B 96.591 1995 66 2 592 2585 388368508 388366515 0 3306
14 TraesCS3B01G363900 chr6B 95.984 1992 78 2 592 2581 588838077 588840068 0 3234
15 TraesCS3B01G363900 chr6B 97.980 594 12 0 1 594 388177394 388176801 0 1031
16 TraesCS3B01G363900 chrUn 98.485 594 9 0 1 594 273321806 273321213 0 1048
17 TraesCS3B01G363900 chrUn 98.485 594 9 0 1 594 404560500 404561093 0 1048
18 TraesCS3B01G363900 chr6A 97.997 599 7 1 1 594 608885504 608886102 0 1035


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G363900 chr3B 575753606 575756190 2584 True 4774.0 4774 100.0000 1 2585 1 chr3B.!!$R1 2584
1 TraesCS3B01G363900 chr7A 60105879 60108502 2623 True 2240.5 3450 97.9375 1 2585 2 chr7A.!!$R1 2584
2 TraesCS3B01G363900 chr5A 73030086 73032709 2623 False 2238.0 3450 97.8530 1 2585 2 chr5A.!!$F1 2584
3 TraesCS3B01G363900 chr1B 638748892 638751515 2623 True 2226.5 3422 97.8120 1 2585 2 chr1B.!!$R1 2584
4 TraesCS3B01G363900 chr2D 637320013 637322006 1993 True 3406.0 3406 97.4940 592 2585 1 chr2D.!!$R1 1993
5 TraesCS3B01G363900 chr2D 189854086 189856079 1993 False 3297.0 3297 96.5400 592 2582 1 chr2D.!!$F1 1990
6 TraesCS3B01G363900 chr2D 635050985 635051583 598 False 1024.0 1024 97.6630 1 594 1 chr2D.!!$F2 593
7 TraesCS3B01G363900 chr3D 523758739 523760732 1993 False 3362.0 3362 97.0930 592 2585 1 chr3D.!!$F1 1993
8 TraesCS3B01G363900 chr2B 500712613 500715236 2623 False 2188.0 3334 97.5790 1 2585 2 chr2B.!!$F1 2584
9 TraesCS3B01G363900 chr6B 388366515 388368508 1993 True 3306.0 3306 96.5910 592 2585 1 chr6B.!!$R2 1993
10 TraesCS3B01G363900 chr6B 588838077 588840068 1991 False 3234.0 3234 95.9840 592 2581 1 chr6B.!!$F1 1989
11 TraesCS3B01G363900 chr6B 388176801 388177394 593 True 1031.0 1031 97.9800 1 594 1 chr6B.!!$R1 593
12 TraesCS3B01G363900 chrUn 273321213 273321806 593 True 1048.0 1048 98.4850 1 594 1 chrUn.!!$R1 593
13 TraesCS3B01G363900 chrUn 404560500 404561093 593 False 1048.0 1048 98.4850 1 594 1 chrUn.!!$F1 593
14 TraesCS3B01G363900 chr6A 608885504 608886102 598 False 1035.0 1035 97.9970 1 594 1 chr6A.!!$F1 593

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
692 737 0.178975 TTAATTAGCCGGCCCATGGG 60.179 55.0 27.87 27.87 38.57 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2093 2140 2.416027 CGCGGTGATCTTCTCTCTTTCA 60.416 50.0 0.0 0.0 0.0 2.69 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 2.151202 TCGCATCTTCTTCGGCTTTTT 58.849 42.857 0.00 0.00 0.00 1.94
378 384 2.159014 GGTATCGTTCACCACATGCCTA 60.159 50.000 0.00 0.00 36.01 3.93
384 390 3.544684 GTTCACCACATGCCTATGATCA 58.455 45.455 0.00 0.00 37.73 2.92
416 422 5.129815 TCAAGCTAGGTTTGGTATCGGTATT 59.870 40.000 3.96 0.00 0.00 1.89
427 433 3.133362 GGTATCGGTATTGGTGAAGTCCA 59.867 47.826 0.00 0.00 35.49 4.02
531 537 5.899547 TCTCTAGATAGATGGGCAGAACAAA 59.100 40.000 0.00 0.00 0.00 2.83
689 734 3.237268 TGAATTAATTAGCCGGCCCAT 57.763 42.857 26.15 13.14 0.00 4.00
692 737 0.178975 TTAATTAGCCGGCCCATGGG 60.179 55.000 27.87 27.87 38.57 4.00
919 965 1.069296 CACTTCTTTTGATTCGGCGCA 60.069 47.619 10.83 0.00 0.00 6.09
968 1014 4.868171 TCGGTTCGATCAACTATCCTTTTG 59.132 41.667 0.00 0.00 35.06 2.44
1182 1229 6.514012 TTTGGAGAATTGGCTATGGAGATA 57.486 37.500 0.00 0.00 0.00 1.98
1251 1298 2.028930 AGCAGGAAAGTCGTTTCGATCT 60.029 45.455 0.00 0.00 42.78 2.75
1504 1551 5.160607 TCGAGGGTTCAATGTGACTATTT 57.839 39.130 0.00 0.00 0.00 1.40
1506 1553 6.001460 TCGAGGGTTCAATGTGACTATTTTT 58.999 36.000 0.00 0.00 0.00 1.94
1548 1595 6.249951 AGATGAGACTTTACTACTGTGGAGT 58.750 40.000 0.00 0.00 36.07 3.85
1647 1694 0.586319 TTGCTCGCGGCTAAATATGC 59.414 50.000 18.14 5.43 42.39 3.14
1789 1836 2.119484 ATTTTCACGGGTCGCCCTCA 62.119 55.000 12.26 0.00 42.67 3.86
1861 1908 3.679917 GCATCTCGAGGTTCTTTGATGGA 60.680 47.826 13.56 0.00 33.89 3.41
1884 1931 7.039882 GGACATAAAGAAATCGTCTTGGTAGA 58.960 38.462 0.00 0.00 46.36 2.59
1980 2027 0.037975 GCTCCCGACCGAAACTAACA 60.038 55.000 0.00 0.00 0.00 2.41
2085 2132 6.489361 CCAGACATAGACTACGTAAAGGGTAT 59.511 42.308 0.00 0.00 0.00 2.73
2247 2297 3.515502 CCCACCATTGAAGTCAGAGTCTA 59.484 47.826 0.00 0.00 0.00 2.59
2503 2554 1.741145 GTTTACATACAACCGGGGCAG 59.259 52.381 6.32 0.00 0.00 4.85
2518 2569 2.952310 GGGGCAGAGTGGTTTATGATTC 59.048 50.000 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 3.493334 TGACTGAAGGAAAGACCGTAGA 58.507 45.455 0.00 0.00 44.74 2.59
378 384 5.840149 ACCTAGCTTGAGAGAGATTGATCAT 59.160 40.000 0.00 0.00 0.00 2.45
384 390 4.534103 ACCAAACCTAGCTTGAGAGAGATT 59.466 41.667 0.00 0.00 0.00 2.40
416 422 5.323581 TCAATTCAATGATGGACTTCACCA 58.676 37.500 0.00 0.00 44.41 4.17
427 433 6.600822 CCACTCTACCACTTCAATTCAATGAT 59.399 38.462 0.00 0.00 0.00 2.45
650 695 2.844348 TCAAGTAATTCCTGGAGGGGAC 59.156 50.000 0.00 0.00 34.78 4.46
689 734 5.045432 AGGTTAAGTTCGATATTTCACCCCA 60.045 40.000 0.00 0.00 0.00 4.96
904 949 5.510671 AGTTATTATGCGCCGAATCAAAAG 58.489 37.500 4.18 0.00 0.00 2.27
919 965 9.444600 AAACCAACATCAAGTACGAGTTATTAT 57.555 29.630 0.00 0.00 0.00 1.28
968 1014 2.271800 CACTGTGAACTATCCGCTTCC 58.728 52.381 0.32 0.00 0.00 3.46
1006 1053 3.896888 AGTGGAAACATCATGGCTTTTCA 59.103 39.130 12.76 3.18 46.14 2.69
1054 1101 4.274214 CAGTTTGAGCAACAGATCTTGACA 59.726 41.667 0.00 0.00 37.93 3.58
1059 1106 5.180868 GTGATTCAGTTTGAGCAACAGATCT 59.819 40.000 0.00 0.00 37.93 2.75
1165 1212 5.391310 CGCACAATATCTCCATAGCCAATTC 60.391 44.000 0.00 0.00 0.00 2.17
1182 1229 2.768253 TGAATCTCTGACCGCACAAT 57.232 45.000 0.00 0.00 0.00 2.71
1504 1551 6.431543 TCATCTTTTGTATTGGCCGAAGTAAA 59.568 34.615 0.00 0.00 0.00 2.01
1506 1553 5.492895 TCATCTTTTGTATTGGCCGAAGTA 58.507 37.500 0.00 0.00 0.00 2.24
1567 1614 4.325109 GGCATCTTACTTAGTTTCCCCCTT 60.325 45.833 0.00 0.00 0.00 3.95
1647 1694 6.998258 AATTTGAAAGCTTTCGTCTCAATG 57.002 33.333 29.03 0.00 40.01 2.82
1789 1836 3.251004 GTGAAAGAACTCAACTGCGGAAT 59.749 43.478 0.00 0.00 0.00 3.01
1861 1908 8.718734 GTTTCTACCAAGACGATTTCTTTATGT 58.281 33.333 0.00 0.00 42.37 2.29
1884 1931 5.941555 TTGTTCTATTGGTTTGGTGGTTT 57.058 34.783 0.00 0.00 0.00 3.27
2093 2140 2.416027 CGCGGTGATCTTCTCTCTTTCA 60.416 50.000 0.00 0.00 0.00 2.69
2247 2297 7.444299 TCCGTATTAGTAAGAAAAACACACCT 58.556 34.615 0.00 0.00 0.00 4.00
2308 2359 3.069289 GGGTTCTACCAACGAAACGAAT 58.931 45.455 0.00 0.00 41.02 3.34
2503 2554 7.226325 CCTCTGAGATTGAATCATAAACCACTC 59.774 40.741 8.03 0.00 0.00 3.51
2518 2569 7.747155 AATGATAAGAATGCCTCTGAGATTG 57.253 36.000 6.17 0.00 33.37 2.67


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.